There is no "normal" JavaScript.
There is the JavaScript Core, and application-specific extensions. What is usually understood as "normal" JavaScript is the Core plus extensions for webbrowsers. Acrobat JavaScript is the Core plus extensions for Acrobat/PDF.
The fundamental difference is in the application and the respective object models.
With the "alert", in Acrobat JavaScript, it is explicitely part of the Application Object, whereas in webbrowser JavaScript, it is part of the Window object, which is also the Global object.
Hope this can help.
Max Wyss.